HPC and NIRD toolkit user course November 2021

In November 2021, the Metacenter partners Sigma2, UiB, UiO, UiT & NTNU are jointly offering a hands-on course for current and future users of national HPC systems (Saga, Fram, Betzy) and the NIRD Toolkit. The course is open to all users and free of charge.

For individual sessions we list recommended prerequisites. The participants can choose which session they want to attend and you're certainly welcome to just attend all sessions you are interested in. On each course day, we will start at 09:00 and conclude at around 13:00. Each "morning" will include presentations and hands-on time on one of the actual HPC systems or the NIRD Toolkit. We recommend that participants use the afternoon on each day to repeat examples from the morning to get more experience on the systems.

Practical Information

This is an online course via zoom. Participants require access to a computer (not provided by the course organisers) with internet connectivity and pre-installed programs to participate in the video meeting of the course (zoom, might work from a browser), to access the HPC systems (e.g., ssh or Putty), to transfer data to/from an HPC system (e.g., scp or WinSCP) and to access the NIRD Toolkit (web browser).

Note 1, Those who do not have an account on one of the HPC machines or NIRD (storage, Toolkit, ...) yet need to apply for an account. The application page is available here and documentation for the application procedure is available here. You are applying for an HPC account. For the project, please select “NN9987K: Course Resources as a Service #3” (the Project manager will be filled in automatically), choose Saga under Resources, set the Account start date to 2021-10-26 and the Account end date to one week after the course, that is 2021-11-12.

Note 2, In order to use the NIRD Toolkit during the course you will need either a Feide account or a Feide OpenIDP guest account. You can create a Feide OpenIDP guest account at https://openidp.feide.no/. See your eduPersonPrincipalName (eduPPN) at http://innsyn.feide.no .

You can always contact us by sending an email to support@metacenter.no.

If you want to receive further information about training events, and other announcements about IT resources and services for researchers, there are a couple of information channels you can subscribe to:

• users at University of Bergen and affiliated institutes: register to hpcnews@uib.no
  
• users of Sigma2 services: subscribe to Sigma2's newsletter
  

HPC and NIRD Toolkit user course

Dates: November 2, 3, 4 and 5 2021
Time: each day 09:00-13:00 with short breaks
Location: Video meeting (zoom) ,We use HackMD for asking questions (information will be send to registered participants) Note, sessions will be recorded and made publicly available after the course!

Participants may choose the lectures which they are interested in.

Registration

The course is free of charge and is organised by the Metacenter partners Sigma2, UiB, UiO & UiT .

Register your participation here

Agenda

Day 1 - Welcome, Introduction to High Performance Computing - 02.11.2021

Get ready: 08:50-09:00 Connect to zoom meeting

Prerequisites: Command line experience is necessary for this lesson. We recommend the participants to go through shell-novice, if new to the command line (also known as terminal or shell)

Course material here

Session 1: 09:00-09:55 Welcome, What is HPC, working on HPC System, Scheduling Jobs

Break for 10 minutes

Session 2: 10:05-11:00 Accessing Software, transferring files

Break for 10 minutes

Session 3: 11:10-12:05 Running a parallel job, Using resources effectively

Break for 10 minutes

Session 4: 12:15-12:45 HPC through a web browser

Session Q&A: 12:45-13:00 Questions & Answers

Day 2 - Optimization of codes and Resource Management - 03.11.2021

Prerequisites: Basic HPC knowledge, we recommend participants to attend Day1 sessions

Get ready: 08:50-09:00 Connect to zoom meeting

Session 1: 09:00-09:55 Optimization of codes and batch script part I

Break for 10 minutes

Session 2: 10:05-11:00 Optimization of codes and batch script part II

Break for 10 minutes

Session 3: 11:10-12:05 Optimizing use of memory and CPUs

Break for 10 minutes

Session 4: 12:15-12:45 Profiling memory and CPU resource usage

Session Q&A: 12:50-13:00 Questions & Answers

Day 3 Containers on HPC and NIRD Toolkit 04.11.2021

Get ready: 08:50-09:00 Connect to zoom meeting

Session 1: 09:00-10:20 Containers on HPC

Break for 10 minutes

Session 2: 10:35-11:30 NIRD Toolkit part I

Break for 10 minutes

Session 3: 11:40-12:40 NIRD Toolkit part II

Break for 10 minutes

Session Q&A: 12:40-13:00 Questions & Answers

Day 4 -GPU Computing - 05.11.2021

Get ready: 08:50-09:00 Connect to zoom meeting

Session 1: 09:00-10:20 Introduction to GPU computing part I

Break for 10 minutes

Session 2: 10:35-11:30 Introduction to GPU computing part II

Break for 10 minutes

Session 3: 11:40-12:40 Using GPUs with containers

Break for 10 minutes

Session Q&A: 12:40-13:00 Questions & Answers

Preparing your machine for the course

We assume you have the necessary tools installed on your machine and are able to use them. You need tools to login into a remote machine (e.g., ssh or PuTTY) and to transfer data to/from a remote machine (e.g., scp or WinSCP). If you need to install such tools, please see the pages of our course in October 2020.

Previous Course

Our previous course page can be found [[1]] and video recording of the course will updated soon.